Merge pull request #106 from sneumann/master

Please pull our changes

DESCRIPTION

 Package: RMassBank
 Type: Package
-Title: Workflow to process tandem MS files and build MassBank records
+Title: Workflow to process tandem MS files and build MassBank records
 Version: 1.9.2.1
 Authors@R: c(
     person(given = "RMassBank at Eawag", email = "massbank@eawag.ch",

NAMESPACE

@@ -63,6 +63,7 @@ export(makeMollist)
 export(makeRecalibration)
 export(mbWorkflow)
 export(msmsRead)
+export(msmsRead.RAW)
 export(msmsWorkflow)
 export(multiply.formula)
 export(newMbWorkspace)

R/RmbWorkspace.R

@@ -261,9 +261,15 @@ setMethod("show", "msmsWorkspace",
 								return(sapply(x$msmsdata, function(x) length(unique(x$childFilt[,1]))))
 							})
 							
-							PeakMat <- matrix(dummy1-dummy2,numspecs,numspecs)
+							whichok <- which(sapply(dummy1,length) != 0)
+							anyok <- whichok[1]
 							
-							tempids <- ids
+							dummy2 <- matrix(unlist(dummy2), ncol = length(dummy1[[anyok]]), byrow = TRUE)
+							dummy1 <- matrix(unlist(dummy1), ncol = length(dummy1[[anyok]]), byrow = TRUE)
+							
+							PeakMat <- dummy1-dummy2
+							
+							tempids <- ids[whichok]
 							cat("Peaks without annotation:\n")
 							sapply(split(PeakMat, rep(1:nrow(PeakMat), each = ncol(PeakMat))), function(x){
 								cat(" -", tempids[1], "\t number of peaks filtered:", x, "\n")
@@ -317,10 +323,16 @@ setMethod("show", "msmsWorkspace",
 																		sapply(x$msmsdata, function(x) length(unique(x$childFilt[,1]))), "\n")
 																		return(sapply(x$msmsdata, function(x) length(unique(x$childFilt[,1]))))
 																	})
-																	
-							PeakMat <- matrix(dummy4-dummy5,numspecs,numspecs)
 							
-							tempids <- ids
+							whichok <- which(sapply(dummy4,length) != 0)
+							anyok <- whichok[1]
+							
+							dummy5 <- matrix(unlist(dummy5), ncol = length(dummy4[[anyok]]), byrow = TRUE)
+							dummy4 <- matrix(unlist(dummy4), ncol = length(dummy4[[anyok]]), byrow = TRUE)
+							
+							PeakMat <- dummy4-dummy5
+							
+							tempids <- ids[whichok]
 							cat("Peaks without annotation in reanalyzed recalibrated peaks:\n")
 							sapply(split(PeakMat, rep(1:nrow(PeakMat), each = ncol(PeakMat))), function(x){
 								cat(" -", tempids[1], "\t number of peaks filtered:", x, "\n")
@@ -420,7 +432,7 @@ plotMbWorkspaces <- function(w1, w2=NULL){
 			lapply(x,function(y) y[['PK$PEAK']][,c("m/z","rel.int.")])
 		})
 		plot_title <- lapply(w2@compiled_ok,function(x){
-			lapply(x,function(y) y[['RECORD_TITLE']])
+			lapply(x,function(y) y[['ACCESSION']])
 		})
 	}
 	
@@ -431,7 +443,7 @@ plotMbWorkspaces <- function(w1, w2=NULL){
 	})
 	
 	plot_title <- lapply(w1@compiled_ok,function(x){
-		lapply(x,function(y) y[['RECORD_TITLE']])
+		lapply(x,function(y) y[['ACCESSION']])
 	})
 	
 	

R/createMassBank.R

@@ -52,6 +52,19 @@ loadInfolist <- function(mb, fileName)
   # Legacy check for loading the Uchem format files.
   # Even if dbname_* are not used downstream of here, it's still good to keep them
   # for debugging reasons.
+  n <- colnames(mbdata_new)
+  cols <- c("id","dbcas","dataused")
+  
+  # Check if comma-separated or semicolon-separated
+  d <- setdiff(cols, n)
+  if(length(d)>0){
+		mbdata_new <- read.csv2(fileName, stringsAsFactors=FALSE)
+		n <- colnames(mbdata_new)
+		d2 <- setdiff(cols, n)
+		if(length(d2) > 0){
+			stop("Some columns are missing in the infolist.")
+		}
+	}
   if("dbname_d" %in% colnames(mbdata_new))
   {
     colnames(mbdata_new)[[which(colnames(mbdata_new)=="dbname_d")]] <- "dbname"
@@ -385,7 +398,7 @@ gatherData <- function(id)
 		# Actually retrieve data from CTS (see the webaccess scripts)
 		infos <- getCtsRecord(inchikey_split)
 		
-		if(length(infos) == 0)
+		if(infos[1] == "Sorry, we couldn't find any matching results")
 			dataUsed <- "dbname"
 		else
 			dataUsed <- "smiles"
@@ -1551,6 +1564,8 @@ addPeaks <- function(mb, filename_or_dataframe)
 	cols <- c("cpdID", "scan", "mzFound", "int", "OK")
 	
 	n <- colnames(df)
+	
+	# Check if comma-separated or semicolon-separated
 	d <- setdiff(cols, n)
 	
 	if(length(d)>0){

R/leMsMs.r

@@ -88,6 +88,16 @@ msmsWorkflow <- function(w, mode="pH", steps=c(1:8), confirmMode = FALSE, newRec
   nProg <- 0
   nLen <- length(w@files)
   
+  if(readMethod == "minimal"){
+	##Edit options
+	opt <- getOption("RMassBank")
+	opt$recalibrator$MS1 <- "recalibrate.identity"
+	opt$recalibrator$MS2 <- "recalibrate.identity"
+	options(RMassBank=opt)
+	##Edit analyzemethod
+	analyzeMethod <- "intensity"
+  }
+  
   # Step 1: acquire all MSMS spectra from files
   if(1 %in% steps)
   {
@@ -151,9 +161,11 @@ msmsWorkflow <- function(w, mode="pH", steps=c(1:8), confirmMode = FALSE, newRec
 	##	names(w@specs) <- basename(as.character(w@files))
 	##}
 		
-	if(readMethod == "peaklist"){
-		splitfn <- strsplit(w@files,'_')
-		cpdIDs <- sapply(splitfn, function(splitted){as.numeric(return(splitted[2]))})
+	if((readMethod == "peaklist") || (readMethod == "minimal")){
+		splitfn <- strsplit(basename(w@files), "_")
+		cpdIDs <- sapply(splitfn, function(splitted) {
+			as.numeric(return(splitted[2]))
+		})
 		files <- list()
 		for(i in 1:length(unique(cpdIDs))) {
 			indices <- sapply(splitfn,function(a){return(unique(cpdIDs)[i] %in% a)})
@@ -1743,7 +1755,7 @@ filterPeaksMultiplicity <- function(peaks, formulacol, recalcBest = TRUE)
 	# rename (because "formulacol" is not the actually correct name)
 	colnames(multInfo) <- c("cpdID", formulacol, "formulaMultiplicity")
 	
-	if(nrow(peaks) == 0)
+	if(!is.data.frame(peaks))
 	{
 		message("filterPeaksMultiplicity: no peaks to aggregate")
 		peaks <- cbind(peaks, data.frame(formulaMultiplicity=numeric()))

R/leMsmsRaw.R

+## For generating the NAMESPACE
 #' @import mzR
-#' @importClassesFrom mzR
-#' @importMethodsFrom mzR
+# # importClassesFrom mzR ## Causes error 
+# # importMethodsFrom mzR 
+#' @import Rcpp ## Was not in manually written NAMESPACE ?
+#' @import RCurl 
+#' @import XML 
+#' @import methods 
+#' @import mzR 
+#' @import rcdk 
+#' @import rjson 
+#' @import yaml 
 NULL # This is required so that roxygen knows where the first manpage starts
 
 #' Extract MS/MS spectra for specified precursor
@@ -15,7 +24,7 @@ NULL # This is required so that roxygen knows where the first manpage starts
 #' 		is a low-level function which uses the mass directly for lookup and is intended for
 #' 		use as a standalone function in unrelated applications.
 #' 
-#' @Usage findMsMsHR(fileName, cpdID, mode="pH",confirmMode =0, useRtLimit = TRUE,
+#' @usage findMsMsHR(fileName, cpdID, mode="pH",confirmMode =0, useRtLimit = TRUE,
 #' 		ppmFine = getOption("RMassBank")$findMsMsRawSettings$ppmFine,
 #' 		mzCoarse = getOption("RMassBank")$findMsMsRawSettings$mzCoarse,
 #' 		fillPrecursorScan = getOption("RMassBank")$findMsMsRawSettings$fillPrecursorScan,
@@ -307,7 +316,7 @@ findMsMsHRperxcms.direct <- function(fileName, cpdID, mode="pH", findPeaksArgs =
 	if(MSe == FALSE){
 		## Fake MS1 from MSn scans
 		## xrmsmsAsMs <- msn2xcmsRaw(xrmsms)
-		suppressWarnings(xrs <- split(msn2xcmsRaw(xrmsms), f=xrmsms@msnCollisionEnergy))
+		suppressWarnings(xrs <- split(msn2xcmsRaw(xrmsms), f = xrmsms@msnCollisionEnergy))
 	} else{
 		xrs <- list()
 		xrs[[1]] <- xrmsms
@@ -320,7 +329,6 @@ findMsMsHRperxcms.direct <- function(fileName, cpdID, mode="pH", findPeaksArgs =
 	psp <- list()
 	spectra <- list()
 	whichmissing <- vector()
-	
 	metaspec <- list()
 	for(ID in 1:length(cpdID)){
 		spectra <- list()
@@ -701,7 +709,7 @@ addMB <- function(w, cpdID, fileName, mode){
 #' @examples \dontrun{
 #' 		c.msmsWSspecs(w1,w2)
 #' }
-#'export
+#'@export
 c.msmsWSspecs <- function(w1 = NA, w2 = NA){
 
 	if(class(w1) != "msmsWorkspace" || class(w2) != "msmsWorkspace"){
@@ -738,4 +746,4 @@ c.msmsWSspecs <- function(w1 = NA, w2 = NA){
 		}
 	}
 	return(w1)
-}
\ No newline at end of file
+}

R/msmsRead.R

@@ -8,8 +8,8 @@
 #' workflow.
 #' 
 #' @param w A \code{msmsWorkspace} to work with.
-#' @param filetable The path to a .csv-file that contains the columns "files" and "cpdid" supplying
-#' 			the relationships between files and compound IDs. Either this or "files" need
+#' @param filetable The path to a .csv-file that contains the columns "Files" and "ID" supplying
+#' 			the relationships between files and compound IDs. Either this or the parameter "files" need
 #'			to be specified. 
 #' @param files A vector or list containing the filenames of the files that are to be read as spectra. 
 #'				For the IDs to be inferred from the filenames alone, there need to be exactly 2 underscores.
@@ -34,6 +34,7 @@
 #' @param progressbar The progress bar callback to use. Only needed for specialized applications.
 #' 			Cf. the documentation of \code{\link{progressBarHook}} for usage.
 #' @param MSe A boolean value that determines whether the spectra were recorded using MSe or not
+#' @param plots A boolean value that determines whether the pseudospectra in XCMS should be plotted
 #' @return The \code{msmsWorkspace} with msms-spectra read.
 #' @seealso \code{\link{msmsWorkspace-class}}, \code{\link{msmsWorkflow}}
 #' @author Michael Stravs, Eawag <michael.stravs@@eawag.ch>
@@ -41,7 +42,7 @@
 #' @export
 msmsRead <- function(w, filetable = NULL, files = NULL, cpdids = NULL, 
 					readMethod, mode, confirmMode = FALSE, useRtLimit = TRUE, 
-					Args = NULL, settings = getOption("RMassBank"), progressbar = "progressBarHook", MSe = FALSE){
+					Args = NULL, settings = getOption("RMassBank"), progressbar = "progressBarHook", MSe = FALSE, plots = FALSE){
 	
 	##Read the files and cpdids according to the definition
 	##All cases are silently accepted, as long as they can be handled according to one definition
@@ -74,7 +75,7 @@ msmsRead <- function(w, filetable = NULL, files = NULL, cpdids = NULL,
 	if(length(w@files) != length(cpdids)){
 		stop("There are a different number of cpdids than files")
 	}
-	if(!(readMethod %in% c("mzR","peaklist","xcms"))){
+	if(!(readMethod %in% c("mzR","peaklist","xcms","minimal"))){
 		stop("The supplied method does not exist")
 	}
 	if(!all(file.exists(w@files))){
@@ -82,6 +83,16 @@ msmsRead <- function(w, filetable = NULL, files = NULL, cpdids = NULL,
 	}
 
 	##This should work
+	if(readMethod == "minimal"){
+		##Edit options
+		opt <- getOption("RMassBank")
+		opt$recalibrator$MS1 <- "recalibrate.identity"
+		opt$recalibrator$MS2 <- "recalibrate.identity"
+		options(RMassBank=opt)
+		##Edit analyzemethod
+		analyzeMethod <- "intensity"
+	}
+	
 	if(readMethod == "mzR"){
 		##Progressbar
 		nLen <- length(w@files)
@@ -110,7 +121,7 @@ msmsRead <- function(w, filetable = NULL, files = NULL, cpdids = NULL,
 	}
 	
 	##Peaklist-readmethod 
-	if(readMethod == "peaklist"){
+	if((readMethod == "peaklist") || (readMethod=="minimal")){
 		w <- createSpecsFromPeaklists(w, cpdids, filenames=w@files, mode=mode)
 		uIDs <- unique(cpdids)
 		files <- list()
@@ -153,7 +164,7 @@ msmsRead <- function(w, filetable = NULL, files = NULL, cpdids = NULL,
 			dummySpecs[[i]] <<- newMsmsWorkspace()
 			dummySpecs[[i]]@specs <<- list()
 			FileIDs <<- cpdids[which(w@files == currfile)]
-			dummylinebreak <- capture.output(metaSpec <<- findMsMsHRperxcms.direct(currfile, FileIDs, mode=mode, findPeaksArgs=Args, MSe = MSe))
+			dummylinebreak <- capture.output(metaSpec <<- findMsMsHRperxcms.direct(currfile, FileIDs, mode=mode, findPeaksArgs=Args, plots, MSe = MSe))
 			
 			for(j in 1:length(FileIDs)){
 				dummySpecs[[i]]@specs[[length(dummySpecs[[i]]@specs)+1]] <<- metaSpec[[j]]
@@ -186,3 +197,130 @@ msmsRead <- function(w, filetable = NULL, files = NULL, cpdids = NULL,
 			return(w)
 	}
 }
+
+#' 
+#' Extracts and processes spectra from a list of xcms-Objects
+#' 
+#' The filenames of the raw LC-MS runs are read from the array \code{files} 
+#' in the global enviroment.
+#' See the vignette \code{vignette("RMassBank")} for further details about the
+#' workflow.
+#' 
+#' @param w A \code{msmsWorkspace} to work with.
+#' @param xRAW A list of xcmsRaw objects whose peaks should be detected and added to the workspace.
+#'				The relevant data must be in the MS1 data of the xcmsRaw object.  You can coerce the
+#'				msn-data in a usable object with the \code{msn2xcmsRaw} function of xcms.
+#' @param cpdids A vector or list containing the compound IDs of the files that are to be read as spectra.
+#'				The ordering of this and \code{files} implicitly assigns each ID to the corresponding file.
+#'				If this is supplied, then the IDs implicitly named in the filenames are ignored.
+#' @param mode \code{"pH", "pNa", "pM", "mH", "mM", "mFA"} for different ions 
+#' 			([M+H]+, [M+Na]+, [M]+, [M-H]-, [M]-, [M+FA]-).
+#' @param findPeaksArgs A list of arguments that will be handed to the xcms-method findPeaks via do.call
+#' @param settings Options to be used for processing. Defaults to the options loaded via
+#' 			\code{\link{loadRmbSettings}} et al. Refer to there for specific settings.
+#' @param progressbar The progress bar callback to use. Only needed for specialized applications.
+#' 			Cf. the documentation of \code{\link{progressBarHook}} for usage.
+#' @param plots A boolean value that determines whether the pseudospectra in XCMS should be plotted
+#' @return The \code{msmsWorkspace} with msms-spectra read.
+#' @seealso \code{\link{msmsWorkspace-class}}, \code{\link{msmsWorkflow}}
+#' @author Michael Stravs, Eawag <michael.stravs@@eawag.ch>
+#' @author Erik Mueller, UFZ
+#' @export
+msmsRead.RAW <- function(w, xRAW = NULL, cpdids = NULL, mode, findPeaksArgs = NULL, 
+							settings = getOption("RMassBank"), progressbar = "progressBarHook", plots = FALSE){
+	
+	require(xcms)
+	
+	##xRAW will be coerced into a list of length 1 if it is an xcmsRaw-object
+	if(class(xRAW) == "xcmsRaw"){
+		xRAW <- list(xRAW)
+	}
+	
+	##Error messages
+	if((class(xRAW) != "list") || any(sapply(xRAW, function(x) class(x) != "xcmsRaw"))){
+		stop("No list of xcmsRaw-objects supplied")
+	}
+	
+	if(is.null(cpdids)){
+		stop("No cpdids supplied")
+	}
+		
+	#msnExist <- which(sapply(xRAW,function(x) length(x@msnPrecursorScan) != 0))
+	#print(length(msnExist))
+	#print(length(xRAW))
+	
+	#if(length(msnExist) != length(xRAW)){
+	#	stop(paste("No msn data in list elements", setdiff(1:length(xRAW),msnExist)))
+	#}
+	
+	require(CAMERA)
+	
+	parentMass <- findMz(cpdids[1], mode=mode)$mzCenter
+	if(is.na(parentMass)){
+		stop(paste("There was no matching entry to the supplied cpdID", cpdids[1] ,"\n Please check the cpdIDs and the compoundlist."))
+	}
+		
+	RT <- findRt(cpdids[1])$RT * 60
+	mzabs <- 0.1
+	
+	getRT <- function(xa) {
+		rt <- sapply(xa@pspectra, function(x) {median(peaks(xa@xcmsSet)[x, "rt"])})
+	}
+	
+	suppressWarnings(setReplicate <- xcmsSet(files=xRAW[[1]]@filepath, method="MS1"))
+	xsmsms <- as.list(replicate(length(xRAW),setReplicate))
+	candidates <- list()
+	anmsms <- list()
+	psp <- list()
+	spectra <- list()
+	whichmissing <- vector()
+	metaspec <- list()
+	for(i in 1:length(xRAW)){
+		devnull <- suppressWarnings(capture.output(peaks(xsmsms[[i]]) <- do.call(findPeaks,c(findPeaksArgs, object = xRAW[[i]]))))
+		
+		if (nrow(peaks(xsmsms[[i]])) == 0) { ##If there are no peaks
+			spectra[[i]] <- matrix(0,2,7)
+			next
+		} else{	
+			## Get pspec 
+			pl <- peaks(xsmsms[[i]])[,c("mz", "rt"), drop=FALSE]
+
+			## Best: find precursor peak
+			candidates[[i]] <- which( pl[,"mz", drop=FALSE] < parentMass + mzabs & pl[,"mz", drop=FALSE] > parentMass - mzabs
+							& pl[,"rt", drop=FALSE] < RT * 1.1 & pl[,"rt", drop=FALSE] > RT * 0.9 )
+			devnull <- capture.output(anmsms[[i]] <- xsAnnotate(xsmsms[[i]]))
+			devnull <- capture.output(anmsms[[i]] <- groupFWHM(anmsms[[i]]))
+
+				if(length(candidates[[i]]) > 0){
+				closestCandidate <- which.min (abs( RT - pl[candidates[[i]], "rt", drop=FALSE]))
+				psp[[i]] <- which(sapply(anmsms[[i]]@pspectra, function(x) {candidates[[i]][closestCandidate] %in% x}))
+				} else{psp[[i]] <- which.min( abs(getRT(anmsms[[i]]) - RT) )}
+				## Now find the pspec for compound       
+
+				## 2nd best: Spectrum closest to MS1
+				##psp <- which.min( abs(getRT(anmsms) - actualRT))
+
+				## 3rd Best: find pspec closest to RT from spreadsheet
+				##psp <- which.min( abs(getRT(anmsms) - RT) )
+				if((plots == TRUE) && (length(psp[[i]]) > 0)){
+					plotPsSpectrum(anmsms[[i]], psp[[i]], log=TRUE,  mzrange=c(0, findMz(cpdids)[[3]]), maxlabel=10)
+				}
+				if(length(psp[[i]]) != 0){
+					spectra[[i]] <- getpspectra(anmsms[[i]], psp[[i]])
+				} else {whichmissing <- c(whichmissing,i)}
+			}
+		}
+		if(length(spectra) != 0){
+			for(i in whichmissing){
+				spectra[[i]] <- matrix(0,2,7)
+			}
+		}
+	if(length(w@specs) != 0){
+		w@specs <- c(w@specs,list(toRMB(spectra,cpdids[1],mode)))
+	} else {
+		w@specs[[1]] <- toRMB(spectra,cpdids[1],mode)
+	}
+	w@files <- c(w@files,xRAW[[1]]@filepath)
+	names(w@specs)[length(w@specs)] <- basename(xRAW[[1]]@filepath)
+	return(w)
+}
\ No newline at end of file

R/settings_example.R

@@ -344,8 +344,23 @@ loadRmbSettings <- function(file_or_list)
 		# Fix the YAML file to suit our needs
 		if(is.null(o$deprofile))
 			o$deprofile <- NA
-		if(is.null(o$babeldir))
+		if(is.null(o$babeldir)){
 			o$babeldir <- NA
+		} else{
+			##Check if babeldir exists
+			babelcheck <- gsub('\"','',o$babeldir)
+			if(substring(babelcheck, nchar(babelcheck)) == "\\"){
+				babelexists <- file.exists(substring(babelcheck, 1, nchar(babelcheck)-1))
+			} else{
+				babelexists <- file.exists(babelcheck)
+			}
+			
+			if(!babelexists){
+				stop("The babeldir does not exist. Please check the babeldir in the settings and adjust it accordingly.")
+			}
+		}
+
+
 		if(nchar(o$annotations$entry_prefix) != 2){
 			stop("The entry prefix must be of length 2")
 		}

R/validateMassBank.R

@@ -2,7 +2,7 @@
 #' 
 #' Validates a plain text MassBank record, or recursively all
 #' records within a directory. The Unit Tests to be used are
-#' installed in RMassBank/inst/unitTests and currently include 
+#' installed in RMassBank/inst/validationTests and currently include 
 #' checks for NAs, peaks versus precursor, precursor mz, 
 #' precursor type, SMILES vs exact mass, total intensities and
 #' title versus type. The validation report is saved as 
@@ -37,12 +37,12 @@ validate <- function(path) {
 	tests <- list()
 	for(i in 1:length(RMassBank.env$mb)){
 		if(RMassBank.env$mb[[i]]@compiled_ok[[1]][['AC$MASS_SPECTROMETRY']][['MS_TYPE']] == "MS2" || RMassBank.env$mb[[i]]@compiled_ok[[1]][['AC$MASS_SPECTROMETRY']][['MS_TYPE']] == "MS"){
-		tests[[i]] <- defineTestSuite(Files[i], dirs = system.file(package="RMassBank", "unitTests"), testFileRegexp = "runit.MS2.test.R",
+		tests[[i]] <- defineTestSuite(Files[i], dirs = system.file(package="RMassBank", "validationTests"), testFileRegexp = "runit.MS2.test.R",
                 #testFuncRegexp = "^test.+",
                 rngKind = "Marsaglia-Multicarry",
                 rngNormalKind = "Kinderman-Ramage")
 		} else{
-			tests[[i]] <- defineTestSuite(Files[i], dirs = system.file(package="RMassBank", "unitTests"), testFileRegexp = "^runit.MSn.test.[rR]$",
+			tests[[i]] <- defineTestSuite(Files[i], dirs = system.file(package="RMassBank", "validationTests"), testFileRegexp = "^runit.MSn.test.[rR]$",
                 #testFuncRegexp = "^test.+",
                 rngKind = "Marsaglia-Multicarry",
                 rngNormalKind = "Kinderman-Ramage")
@@ -140,3 +140,36 @@ smiles2mass <- function(SMILES){
 	mass <- get.exact.mass(massfromformula)
 	return(mass)
 }
+
+.unitTestRMB <- function(){
+	require(RUnit)
+	library(RMassBank)
+	library(RMassBankData)
+	w <- newMsmsWorkspace()
+	RmbDefaultSettings()
+	files <- list.files(system.file("spectra", package="RMassBankData"),
+		 ".mzML", full.names = TRUE)
+	basename(files)
+	# To make the workflow faster here, we use only 2 compounds:
+	w@files <- files
+	loadList(system.file("list/NarcoticsDataset.csv", 
+		package="RMassBankData"))
+	w <- msmsWorkflow(w, mode="pH", steps=c(1:4), archivename = 
+					"pH_narcotics")
+	w <- msmsWorkflow(w, mode="pH", steps=c(5:8), archivename = 
+			"pH_narcotics")	
+	
+	testSuite <- defineTestSuite("Electronic noise and formula calculation Test", dirs = system.file("unitTests", 
+		package="RMassBank"), testFileRegexp = "runit.EN_FC.R",
+					#testFuncRegexp = "^test.+",
+					rngKind = "Marsaglia-Multicarry",
+					rngNormalKind = "Kinderman-Ramage")
+					
+	testData <- suppressWarnings(runTestSuite(testSuite))
+	
+	file.remove("pH_narcotics_Failpeaks.csv")
+	
+	# Prints the HTML-record
+	printTextProtocol(testData)
+	return(testData)
+}

inst/unitTests/runit.EN_FC.R

+test.eletronicnoise <- function(){
+	failpeaks <- read.csv("pH_narcotics_Failpeaks.csv")
+	
+	checkTrue(!any(apply(failpeaks,1,function(x) all(x[2:4] == c(1738,2819,668,201.69144)))))
+}
+
+test.formulacalc <- function(){
+	failpeaks <- read.csv("pH_narcotics_Failpeaks.csv")
+	
+	checkTrue(!any(apply(failpeaks,1,function(x) all(x[2:4] == c(70,2758,321,56.04933)))))
+}
\ No newline at end of file

man/c.msmsWSspecs.Rd

+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/leMsmsRaw.R
+\name{c.msmsWSspecs}
+\alias{c.msmsWSspecs}
+\title{Concatenation of raw spectra in msmsWorkspace}
+\usage{
+c.msmsWSspecs(w1, w2)
+}
+\arguments{
+\item{w1,w2}{The msmsWorkspaces of which the spectra should be concatenated}
+}
+\value{
+The \code{msmsWorkspace} with the spectra of two workspaces concatenated into one. Please note that the spectra from w2 will be concatenated to w1 and not vice versa.
+}
+\description{
+Concatenates the (at)specs spectra of msmsWorkspace according to cpdIDs
+}
+\examples{
+\dontrun{
+		c.msmsWSspecs(w1,w2)
+}
+}
+\author{
+Erik Mueller
+}
+\seealso{
+\code{\link{addPeaksManually}}
+}
+

man/findEIC.Rd

+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/leMsmsRaw.R
 \name{findEIC}
 \alias{findEIC}
 \title{Extract EICs}
 \usage{
-  findEIC(msRaw, mz, limit = NULL, rtLimit = NA,
-    headerCache = NULL)
+findEIC(msRaw, mz, limit = NULL, rtLimit = NA, headerCache = NULL,
+  floatingRecalibration = NULL)
 }
 \arguments{
-  \item{msRaw}{The mzR file handle}
+\item{msRaw}{The mzR file handle}
 
-  \item{mz}{The mass or mass range to extract the EIC for:
-  either a single mass (with the range specified by
-  \code{limit} below) or a mass range in the form of
-  \code{c(min, max)}.}
+\item{mz}{The mass or mass range to extract the EIC for: either a single mass
+(with the range specified by \code{limit} below) or a mass range
+in the form of \code{c(min, max)}.}
 
-  \item{limit}{If a single mass was given for \code{mz}:
-  the mass window to extract.  A limit of 0.001 means that
-  the EIC will be returned for \code{[mz - 0.001, mz +
-  0.001]}.}
+\item{limit}{If a single mass was given for \code{mz}: the mass window to extract.
+A limit of 0.001 means that the EIC will be returned for \code{[mz - 0.001, mz + 0.001]}.}
 
-  \item{rtLimit}{If given, the retention time limits in
-  form \code{c(rtmin, rtmax)} in seconds.}
+\item{rtLimit}{If given, the retention time limits in form \code{c(rtmin, rtmax)} in seconds.}
 
-  \item{headerCache}{If present, the complete
-  \code{mzR::header(msRaw)}. Passing this value is useful
-  if spectra for multiple compounds should be extracted
-  from the same mzML file, since it avoids getting the data
-  freshly from \code{msRaw} for every compound.}
+\item{headerCache}{If present, the complete \code{mzR::header(msRaw)}. Passing
+this value is useful if spectra for multiple compounds should be
+extracted from the same mzML file, since it avoids getting the data
+freshly from \code{msRaw} for every compound.}
+
+\item{floatingRecalibration}{A fitting function that \code{predict()}s a mass shift based on the retention time. Can be used
+if a lockmass calibration is known (however you have to build the calibration yourself.)}
 }
 \value{
-  A \code{[rt, intensity, scan]} matrix (\code{scan} being
-  the scan number.)
+A \code{[rt, intensity, scan]} matrix (\code{scan} being the scan number.)
 }
 \description{
-  Extract EICs from raw data for a determined mass window.
+Extract EICs from raw data for a determined mass window.
 }
 \author{
-  Michael A. Stravs, Eawag <michael.stravs@eawag.ch>
+Michael A. Stravs, Eawag <michael.stravs@eawag.ch>
 }
 \seealso{
-  findMsMsHR
+findMsMsHR
 }
 

man/findMsMsHR.Rd

+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/leMsmsRaw.R
 \name{findMsMsHR}
 \alias{findMsMsHR}
 \alias{findMsMsHR.direct}
 \alias{findMsMsHR.mass}
 \title{Extract MS/MS spectra for specified precursor}
 \usage{
-  findMsMsHR(fileName, cpdID, mode="pH",confirmMode =0,
-    useRtLimit = TRUE, ppmFine =
-    getOption("RMassBank")$findMsMsRawSettings$ppmFine,
-    mzCoarse =
-    getOption("RMassBank")$findMsMsRawSettings$mzCoarse,
-    fillPrecursorScan =
-    getOption("RMassBank")$findMsMsRawSettings$fillPrecursorScan,
-    rtMargin = getOption("RMassBank")$rtMargin, deprofile =
-    getOption("RMassBank")$deprofile)
-
-  findMsMsHR.mass(msRaw, mz, limit.coarse, limit.fine,
-    rtLimits = NA, maxCount = NA, headerCache = NA,
-    fillPrecursorScan = FALSE, deprofile =
-    getOption("RMassBank")$deprofile)
-
-  findMsMsHR.direct(msRaw, cpdID, mode = "pH", confirmMode
-    = 0, useRtLimit = TRUE, ppmFine =
-    getOption("RMassBank")$findMsMsRawSettings$ppmFine,
-    mzCoarse =
-    getOption("RMassBank")$findMsMsRawSettings$mzCoarse,
-    fillPrecursorScan =
-    getOption("RMassBank")$findMsMsRawSettings$fillPrecursorScan,
-    rtMargin = getOption("RMassBank")$rtMargin, deprofile =
-    getOption("RMassBank")$deprofile, headerCache = NA)
+findMsMsHR(fileName, cpdID, mode="pH",confirmMode =0, useRtLimit = TRUE,
+		ppmFine = getOption("RMassBank")$findMsMsRawSettings$ppmFine,
+		mzCoarse = getOption("RMassBank")$findMsMsRawSettings$mzCoarse,
+		fillPrecursorScan = getOption("RMassBank")$findMsMsRawSettings$fillPrecursorScan,
+		rtMargin = getOption("RMassBank")$rtMargin,
+		deprofile = getOption("RMassBank")$deprofile)
+
+		findMsMsHR.mass(msRaw, mz, limit.coarse, limit.fine, rtLimits = NA, maxCount = NA,
+		headerCache = NULL, fillPrecursorScan = FALSE,
+		deprofile = getOption("RMassBank")$deprofile)
+
+findMsMsHR.direct(msRaw, cpdID, mode = "pH", confirmMode = 0, useRtLimit = TRUE,
+			ppmFine = getOption("RMassBank")$findMsMsRawSettings$ppmFine,
+			mzCoarse = getOption("RMassBank")$findMsMsRawSettings$mzCoarse,
+			fillPrecursorScan = getOption("RMassBank")$findMsMsRawSettings$fillPrecursorScan,
+			rtMargin = getOption("RMassBank")$rtMargin,
+			deprofile = getOption("RMassBank")$deprofile, headerCache = NULL)
 }
 \arguments{
-  \item{fileName}{The file to open and search the MS2
-  spectrum in.}
+\item{fileName}{The file to open and search the MS2 spectrum in.}
 
-  \item{msRaw}{The opened raw file (mzR file handle) to
-  search the MS2 spectrum in.}
+\item{cpdID}{The compound ID in the compound list (see \code{\link{loadList}})
+to use for formula lookup.}
 
-  \item{cpdID}{The compound ID in the compound list (see
-  \code{\link{loadList}}) to use for formula lookup.}
+\item{mode}{The processing mode (determines which ion/adduct is searched):
+\code{"pH", "pNa", "pM", "mH", "mM", "mFA"} for different ions
+([M+H]+, [M+Na]+, [M]+, [M-H]-, [M]-, [M+FA]-).}
 
-  \item{mz}{The mass to use for spectrum search.}
+\item{confirmMode}{Whether to use the highest-intensity precursor (=0), second-
+highest (=1), third-highest (=2)...}
 
-  \item{ppmFine}{The limit in ppm to use for fine limit
-  (see below) calculation.}
+\item{useRtLimit}{Whether to respect retention time limits from the compound list.}
 
-  \item{mzCoarse}{The coarse limit to use for locating
-  potential MS2 scans: this tolerance is used when finding
-  scans with a suitable precursor ion value.}
+\item{ppmFine}{The limit in ppm to use for fine limit (see below) calculation.}
 
-  \item{limit.fine}{The fine limit to use for locating MS2
-  scans: this tolerance is used when locating an
-  appropriate analyte peak in the MS1 precursor spectrum.}
+\item{mzCoarse}{The coarse limit to use for locating potential MS2 scans:
+this tolerance is used when finding scans with a suitable precursor
+ion value.}
 
-  \item{limit.coarse}{Parameter in \code{findMsMsHR.mass}
-  corresponding to \code{mzCoarse}.  (The parameters are
-  distinct to clearly conceptually distinguish
-  findMsMsHR.mass (a standalone useful function) from the
-  cpdID based functions (workflow functions).)}
+\item{fillPrecursorScan}{If \code{TRUE}, the precursor scan will be filled from MS1 data.
+To be used for data where the precursor scan is not stored in the raw data.}
 
-  \item{mode}{The processing mode (determines which
-  ion/adduct is searched): \code{"pH", "pNa", "pM", "mH",
-  "mM", "mFA"} for different ions ([M+H]+, [M+Na]+, [M]+,
-  [M-H]-, [M]-, [M+FA]-).}
+\item{rtMargin}{The retention time tolerance to use.}
 
-  \item{confirmMode}{Whether to use the highest-intensity
-  precursor (=0), second- highest (=1), third-highest
-  (=2)...}
+\item{deprofile}{Whether deprofiling should take place, and what method should be
+used (cf. \code{\link{deprofile}})}
 
-  \item{useRtLimit}{Whether to respect retention time
-  limits from the compound list.}
+\item{msRaw}{The opened raw file (mzR file handle) to search the MS2 spectrum in.}
 
-  \item{rtLimits}{\code{c(min, max)}: Minimum and maximum
-  retention time to use when locating the MS2 scans.}
+\item{mz}{The mass to use for spectrum search.}
 
-  \item{headerCache}{If present, the complete
-  \code{mzR::header(msRaw)}. Passing this value is useful
-  if spectra for multiple compounds should be extracted
-  from the same mzML file, since it avoids getting the data
-  freshly from \code{msRaw} for every compound.}
+\item{limit.fine}{The fine limit to use for locating MS2 scans: this tolerance
+is used when locating an appropriate analyte peak in the MS1 precursor
+spectrum.}
 
-  \item{maxCount}{The maximal number of spectra groups to
-  return. One spectra group consists of all data-dependent
-  scans from the same precursor whose precursor mass
-  matches the specified search mass.}
+\item{limit.coarse}{Parameter in \code{findMsMsHR.mass} corresponding to \code{mzCoarse}.
+(The parameters are distinct to clearly conceptually distinguish findMsMsHR.mass
+(a standalone useful function) from the cpdID based functions (workflow functions).)}
 
-  \item{fillPrecursorScan}{If \code{TRUE}, the precursor
-  scan will be filled from MS1 data.  To be used for data
-  where the precursor scan is not stored in the raw data.}
+\item{rtLimits}{\code{c(min, max)}: Minimum and maximum retention time to use
+when locating the MS2 scans.}
 
-  \item{rtMargin}{The retention time tolerance to use.}
+\item{headerCache}{If present, the complete \code{mzR::header(msRaw)}. Passing
+this value is useful if spectra for multiple compounds should be
+extracted from the same mzML file, since it avoids getting the data
+freshly from \code{msRaw} for every compound.}
 
-  \item{deprofile}{Whether deprofiling should take place,
-  and what method should be used (cf.
-  \code{\link{deprofile}})}
+\item{maxCount}{The maximal number of spectra groups to return. One spectra group
+consists of all data-dependent scans from the same precursor whose precursor
+mass matches the specified search mass.}
 }
 \value{
-  For \code{findMsMsHR} and \code{findMsMsHR.direct}: A
-  "spectrum set", a list with items:
-  \item{foundOK}{\code{TRUE} if a spectrum was found,
-  \code{FALSE} otherwise.  Note: if \code{FALSE}, all other
-  values can be missing!} \item{parentScan}{The scan number
-  of the precursor scan.} \item{parentHeader}{The header
-  row of the parent scan, as returned by
-  \code{mzR::header}.} \item{childScans}{The scan numbers
-  of the data-dependent MS2 scans.} \item{childHeaders}{The
-  header rows of the MS2 scan, as returned by
-  \code{mzR::header}.} \item{parentPeak}{The MS1 precursor
-  spectrum as a 2-column matrix} \item{peaks}{A list of
-  2-column \code{mz, int} matrices of the MS2 scans.} For
-  \code{findMsMsHR.mass}: a list of "spectrum sets" as
-  defined above, sorted by decreasing precursor intensity.
+For \code{findMsMsHR} and \code{findMsMsHR.direct}: A "spectrum set", a list with items:
+			\item{foundOK}{\code{TRUE} if a spectrum was found, \code{FALSE} otherwise.
+				Note: if \code{FALSE}, all other values can be missing!}
+			\item{parentScan}{The scan number of the precursor scan.}
+			\item{parentHeader}{The header row of the parent scan, as returned by
+				\code{mzR::header}.}
+			\item{childScans}{The scan numbers of the data-dependent MS2 scans.}
+			\item{childHeaders}{The header rows of the MS2 scan, as returned by
+				\code{mzR::header}.}
+			\item{parentPeak}{The MS1 precursor spectrum as a 2-column matrix}
+			\item{peaks}{A list of  2-column \code{mz, int} matrices of the MS2 scans.}
+			For \code{findMsMsHR.mass}: a list of "spectrum sets" as defined above, sorted
+			by decreasing precursor intensity.
 }
 \description{
-  Extracts MS/MS spectra from LC-MS raw data for a
-  specified precursor, specified either via the RMassBank
-  compound list (see \code{\link{loadList}}) or via a mass.
+Extracts MS/MS spectra from LC-MS raw data for a specified precursor, specified
+either via the RMassBank compound list (see \code{\link{loadList}}) or via a mass.
 }
 \details{
-  Different versions of the function get the data from
-  different sources. Note that findMsMsHR and
-  findMsMsHR.direct differ mainly in that findMsMsHR opens
-  a file whereas findMsMs.direct uses an open file handle -
-  both are intended to be used in a full process which
-  involves compound lists etc. In contrast, findMsMsHR.mass
-  is a low-level function which uses the mass directly for
-  lookup and is intended for use as a standalone function
-  in unrelated applications.
+Different versions of the function get the data from different sources. Note that
+		findMsMsHR and findMsMsHR.direct differ mainly in that findMsMsHR opens a file
+		whereas findMsMs.direct uses an open file handle - both are intended to be used
+		in a full process which involves compound lists etc. In contrast, findMsMsHR.mass
+		is a low-level function which uses the mass directly for lookup and is intended for
+		use as a standalone function in unrelated applications.
 }
 \examples{
 \dontrun{
@@ -142,9 +119,9 @@
 }
 }
 \author{
-  Michael A. Stravs, Eawag <michael.stravs@eawag.ch>
+Michael A. Stravs, Eawag <michael.stravs@eawag.ch>
 }
 \seealso{
-  findEIC
+findEIC
 }
 

man/mbWorkspace-class.Rd

-\docType{class}
-\name{mbWorkspace-class}
-\alias{mbWorkspace-class}
-\alias{show,mbWorkspace-method}
-\title{Workspace for \code{mbWorkflow} data}
-\description{
-  A workspace which stores input and output data for use
-  with \code{mbWorkflow}.
-}
-\details{
-  Slots: \describe{ \item{aggregatedRcSpecs,
-  refilteredRcSpecs}{The corresponding input data from
-  \code{\link{msmsWorkspace-class}}}
-  \item{additionalPeaks}{A list of additional peaks which
-  can be loaded using \code{\link{addPeaks}}.}
-  \item{mbdata, mbdata_archive, mbdata_relisted}{Infolist
-  data: Data for annotation of MassBank records, which can
-  be loaded using \code{\link{loadInfolists}}.}
-  \item{compiled, compiled_ok}{ Compiled tree-structured
-  MassBank records. \code{compiled_ok} contains only the
-  compounds with at least one valid spectrum.}
-  \item{mbfiles}{Compiled MassBank records in text
-  representation.} \item{molfile}{MOL files with the
-  compound structures.} \item{ok,problems}{Index lists for
-  internal use which denote which compounds have valid
-  spectra.} }
-
-  Methods: \describe{ \item{show}{Shows a brief summary of
-  the object. Currently only a stub.} }
-}
-\author{
-  Michael Stravs, Eawag <michael.stravs@eawag.ch>
-}
-\seealso{
-  \code{\link{mbWorkflow}}
-}
-
+\docType{class}
+\name{mbWorkspace-class}
+\alias{mbWorkspace-class}
+\alias{show,mbWorkspace-method}
+\title{Workspace for \code{mbWorkflow} data}
+\description{
+A workspace which stores input and output data for use with \code{mbWorkflow}.
+
+
+}
+\details{
+Slots:
+ \describe{
+	\item{aggregatedRcSpecs, refilteredRcSpecs}{The corresponding
+		 input data from \code{\link{msmsWorkspace-class}}}
+ \item{additionalPeaks}{A list of additional peaks which can be loaded
+		using \code{\link{addPeaks}}.}
+ \item{mbdata, mbdata_archive, mbdata_relisted}{Infolist data: Data for
+		annotation of MassBank records, which can be loaded using
+		\code{\link{loadInfolists}}.}
+ \item{compiled, compiled_ok}{
+		Compiled tree-structured MassBank records. \code{compiled_ok} contains
+		only the compounds with at least one valid spectrum.}
+ \item{mbfiles}{Compiled MassBank records in text representation.}
+ \item{molfile}{MOL files with the compound structures.}
+ \item{ok,problems}{Index lists for internal use which denote which compounds
+		have valid spectra.}
+}
+
+Methods:
+\describe{
+		\item{show}{Shows a brief summary of the object. Currently only a stub.}
+}
+}
+\author{
+Michael Stravs, Eawag <michael.stravs@eawag.ch>
+}
+\seealso{
+\code{\link{mbWorkflow}}
+}
+

man/msmsRead.RAW.Rd

+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/msmsRead.R
+\name{msmsRead.RAW}
+\alias{msmsRead.RAW}
+\title{Extracts and processes spectra from a list of xcms-Objects}
+\usage{
+msmsRead.RAW(w, xRAW = NULL, cpdids = NULL, mode, findPeaksArgs = NULL,
+  settings = getOption("RMassBank"), progressbar = "progressBarHook",
+  plots = FALSE)
+}
+\arguments{
+\item{w}{A \code{msmsWorkspace} to work with.}
+
+\item{xRAW}{A list of xcmsRaw objects whose peaks should be detected and added to the workspace.
+The relevant data must be in the MS1 data of the xcmsRaw object.  You can coerce the
+msn-data in a usable object with the \code{msn2xcmsRaw} function of xcms.}
+
+\item{cpdids}{A vector or list containing the compound IDs of the files that are to be read as spectra.
+The ordering of this and \code{files} implicitly assigns each ID to the corresponding file.
+If this is supplied, then the IDs implicitly named in the filenames are ignored.}
+
+\item{mode}{\code{"pH", "pNa", "pM", "mH", "mM", "mFA"} for different ions
+([M+H]+, [M+Na]+, [M]+, [M-H]-, [M]-, [M+FA]-).}
+
+\item{findPeaksArgs}{A list of arguments that will be handed to the xcms-method findPeaks via do.call}
+
+\item{settings}{Options to be used for processing. Defaults to the options loaded via
+\code{\link{loadRmbSettings}} et al. Refer to there for specific settings.}
+
+\item{progressbar}{The progress bar callback to use. Only needed for specialized applications.
+Cf. the documentation of \code{\link{progressBarHook}} for usage.}
+
+\item{plots}{A boolean value that determines whether the pseudospectra in XCMS should be plotted}
+}
+\value{
+The \code{msmsWorkspace} with msms-spectra read.
+}
+\description{
+The filenames of the raw LC-MS runs are read from the array \code{files}
+in the global enviroment.
+See the vignette \code{vignette("RMassBank")} for further details about the
+workflow.
+}
+\author{
+Michael Stravs, Eawag <michael.stravs@eawag.ch>
+
+Erik Mueller, UFZ
+}
+\seealso{
+\code{\link{msmsWorkspace-class}}, \code{\link{msmsWorkflow}}
+}
+

man/msmsRead.Rd

+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/msmsRead.R
 \name{msmsRead}
 \alias{msmsRead}
 \title{Extracts and processes spectra from a specified file list, according to
 loaded options and given parameters.}
 \usage{
-  msmsRead(w, filetable = NULL, files = NULL,
-    cpdids = NULL, readMethod, mode, confirmMode = FALSE,
-    useRtLimit = TRUE, Args = NULL,
-    settings = getOption("RMassBank"),
-    progressbar = "progressBarHook", MSe = FALSE)
+msmsRead(w, filetable = NULL, files = NULL, cpdids = NULL, readMethod,
+  mode, confirmMode = FALSE, useRtLimit = TRUE, Args = NULL,
+  settings = getOption("RMassBank"), progressbar = "progressBarHook",
+  MSe = FALSE, plots = FALSE)
 }
 \arguments{
-  \item{w}{A \code{msmsWorkspace} to work with.}
+\item{w}{A \code{msmsWorkspace} to work with.}
 
-  \item{filetable}{The path to a .csv-file that contains
-  the columns "files" and "cpdid" supplying the
-  relationships between files and compound IDs. Either this
-  or "files" need to be specified.}
+\item{filetable}{The path to a .csv-file that contains the columns "Files" and "ID" supplying
+the relationships between files and compound IDs. Either this or the parameter "files" need
+to be specified.}
 
-  \item{files}{A vector or list containing the filenames of
-  the files that are to be read as spectra.  For the IDs to
-  be inferred from the filenames alone, there need to be
-  exactly 2 underscores.}
+\item{files}{A vector or list containing the filenames of the files that are to be read as spectra.
+For the IDs to be inferred from the filenames alone, there need to be exactly 2 underscores.}
 
-  \item{cpdids}{A vector or list containing the compound
-  IDs of the files that are to be read as spectra.  The
-  ordering of this and \code{files} implicitly assigns each
-  ID to the corresponding file.  If this is supplied, then
-  the IDs implicitly named in the filenames are ignored.}
+\item{cpdids}{A vector or list containing the compound IDs of the files that are to be read as spectra.
+The ordering of this and \code{files} implicitly assigns each ID to the corresponding file.
+If this is supplied, then the IDs implicitly named in the filenames are ignored.}
 
-  \item{readMethod}{Several methods are available to get
-  peak lists from the files.  Currently supported are
-  "mzR", "xcms", "MassBank" and "peaklist".  The first two
-  read MS/MS raw data, and differ in the strategy used to
-  extract peaks. MassBank will read existing records, so
-  that e.g. a recalibration can be performed, and
-  "peaklist" just requires a CSV with two columns and the
-  column header "mz", "int".}
+\item{readMethod}{Several methods are available to get peak lists from the files.
+Currently supported are "mzR", "xcms", "MassBank" and "peaklist".
+The first two read MS/MS raw data, and differ in the strategy
+used to extract peaks. MassBank will read existing records,
+so that e.g. a recalibration can be performed, and "peaklist"
+just requires a CSV with two columns and the column header "mz", "int".}
 
-  \item{mode}{\code{"pH", "pNa", "pM", "mH", "mM", "mFA"}
-  for different ions ([M+H]+, [M+Na]+, [M]+, [M-H]-, [M]-,
-  [M+FA]-).}
+\item{mode}{\code{"pH", "pNa", "pM", "mH", "mM", "mFA"} for different ions
+([M+H]+, [M+Na]+, [M]+, [M-H]-, [M]-, [M+FA]-).}
 
-  \item{confirmMode}{Defaults to false (use most intense
-  precursor). Value 1 uses the 2nd-most intense precursor
-  for a chosen ion (and its data-dependent scans) , etc.}
+\item{confirmMode}{Defaults to false (use most intense precursor). Value 1 uses
+the 2nd-most intense precursor for a chosen ion (and its data-dependent scans)
+, etc.}
 
-  \item{useRtLimit}{Whether to enforce the given retention
-  time window.}
+\item{useRtLimit}{Whether to enforce the given retention time window.}
 
-  \item{Args}{A list of arguments that will be handed to
-  the xcms-method findPeaks via do.call}
+\item{Args}{A list of arguments that will be handed to the xcms-method findPeaks via do.call}
 
-  \item{settings}{Options to be used for processing.
-  Defaults to the options loaded via
-  \code{\link{loadRmbSettings}} et al. Refer to there for
-  specific settings.}
+\item{settings}{Options to be used for processing. Defaults to the options loaded via
+\code{\link{loadRmbSettings}} et al. Refer to there for specific settings.}
 
-  \item{progressbar}{The progress bar callback to use. Only
-  needed for specialized applications.  Cf. the
-  documentation of \code{\link{progressBarHook}} for
-  usage.}
+\item{progressbar}{The progress bar callback to use. Only needed for specialized applications.
+Cf. the documentation of \code{\link{progressBarHook}} for usage.}
 
-  \item{MSe}{A boolean value that determines whether the
-  spectra were recorded using MSe or not}
+\item{MSe}{A boolean value that determines whether the spectra were recorded using MSe or not}
+
+\item{plots}{A boolean value that determines whether the pseudospectra in XCMS should be plotted}
 }
 \value{
-  The \code{msmsWorkspace} with msms-spectra read.
+The \code{msmsWorkspace} with msms-spectra read.
 }
 \description{
-  The filenames of the raw LC-MS runs are read from the
-  array \code{files} in the global enviroment. See the
-  vignette \code{vignette("RMassBank")} for further details
-  about the workflow.
+The filenames of the raw LC-MS runs are read from the array \code{files}
+in the global enviroment.
+See the vignette \code{vignette("RMassBank")} for further details about the
+workflow.
 }
 \author{
-  Michael Stravs, Eawag <michael.stravs@eawag.ch>
+Michael Stravs, Eawag <michael.stravs@eawag.ch>
 
-  Erik Mueller, UFZ
+Erik Mueller, UFZ
 }
 \seealso{
-  \code{\link{msmsWorkspace-class}},
-  \code{\link{msmsWorkflow}}
+\code{\link{msmsWorkspace-class}}, \code{\link{msmsWorkflow}}
 }
 

man/msmsWorkspace-class.Rd

-\docType{class}
-\name{msmsWorkspace-class}
-\alias{msmsWorkspace-class}
-\alias{show,msmsWorkspace-method}
-\title{Workspace for \code{msmsWorkflow} data}
-\description{
-  A workspace which stores input and output data for
-  \code{\link{msmsWorkflow}}.
-}
-\details{
-  Slots:
-
-  \describe{ \item{files}{The input file names}
-  \item{specs}{The spectra extracted from the raw files}
-  \item{analyzedSpecs}{The spectra with annotated peaks
-  after workflow step 2.} \item{aggregatedSpecs}{The
-  \code{analyzedSpec} data regrouped and aggregated, after
-  workflow step 3.} \item{rc, rc.ms1}{The recalibration
-  curves generated in workflow step 4.}
-  \item{recalibratedSpecs}{The spectra from \code{specs}
-  recalibrated with the curves from \code{rc, rc,ms1}.}
-  \item{analyzedRcSpecs}{The recalibrated spectra with
-  annotated peaks after workflow step 5.}
-  \item{aggregatedRcSpecs}{The \code{analyzedRcSpec} data
-  regrouped and aggregated, after workflow step 6.}
-  \item{reanalyzedRcSpecs}{The regrouped and aggregated
-  spectra, with added reanalyzed peaks (after step 7, see
-  \code{\link{reanalyzeFailpeaks}}).}
-  \item{refilteredRcSpecs}{Final data to use for MassBank
-  record creation after multiplicity filtering (step 8).} }
-
-  Methods: \describe{ \item{show}{Shows a brief summary of
-  the object. Currently only the included files.} }
-}
-\author{
-  Michael Stravs, Eawag <michael.stravs@eawag.ch>
-}
-\seealso{
-  \code{\link{msmsWorkflow}}
-}
-
+\docType{class}
+\name{msmsWorkspace-class}
+\alias{msmsWorkspace-class}
+\alias{show,msmsWorkspace-method}
+\title{Workspace for \code{msmsWorkflow} data}
+\description{
+A workspace which stores input and output data for \code{\link{msmsWorkflow}}.
+}
+\details{
+Slots:
+
+\describe{
+	\item{files}{The input file names}
+	\item{specs}{The spectra extracted from the raw files}
+ \item{analyzedSpecs}{The spectra with annotated peaks after workflow step 2.}
+ \item{aggregatedSpecs}{The \code{analyzedSpec} data regrouped and aggregated,
+		after workflow step 3.}
+ \item{rc, rc.ms1}{The recalibration curves generated in workflow step 4.}
+ \item{recalibratedSpecs}{The spectra from \code{specs} recalibrated with the curves
+		from \code{rc, rc,ms1}.}
+	\item{analyzedRcSpecs}{The recalibrated spectra with annotated peaks after
+		workflow step 5.}
+	\item{aggregatedRcSpecs}{The \code{analyzedRcSpec} data regrouped and aggregated,
+		after workflow step 6.}
+ \item{reanalyzedRcSpecs}{The regrouped and aggregated spectra, with added reanalyzed
+		peaks (after step 7, see \code{\link{reanalyzeFailpeaks}}).}
+ \item{refilteredRcSpecs}{Final data to use for MassBank record creation after
+		multiplicity filtering (step 8).}
+}
+
+Methods: \describe{
+	\item{show}{Shows a brief summary of the object. Currently only the included files.}
+	}
+}
+\author{
+Michael Stravs, Eawag <michael.stravs@eawag.ch>
+}
+\seealso{
+\code{\link{msmsWorkflow}}
+}
+